Hi Troels,
So it was the tcshrc here was the output
lias rm 'rm -i'
alias cp 'cp -i'
alias mv 'mv -i'
setenv NMR_CONT CORRECT_ALL
setenv GLOVEDIR ~/glove
if (-e /usr/local/NMRPipe/com/nmrInit.linux9.com) then
source /usr/local/NMRPipe/com/nmrInit.linux9.com
endif
set PATH = ($PATH /usr/local/java:$GLOVEDIR/bin)
alias relax '/usr/local/relax-1.3.10/relax -g'
alias csi '/usr/local//csi'
alias nvj '/usr/local/bin/NMRViewJ'
alias pymol '/usr/local/pymol/pymol.exe'
alias nessy '/usr/local/nessy/nessy'
alias relax '/usr/local/Relax/relax-2.2.5/relax -g'
#set prompt="crowlab >"
alias naccess '/usr/local/Naccess/naccess2.1.1/naccess'
if( ${?prompt} ) then
alias setprompt 'set prompt = "crowlab: [%c]> "'
alias cwdcmd 'setprompt'
setprompt
endif
Also, the 2nd command gave me no responce.
crowlab: [~]> alias get 'set noglob; wget
http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_scripts/openmpi_test_install_tcsh.sh;unset
noglob'
crowlab: [~]>
On Mon, Oct 3, 2016 at 9:32 AM, Troels Emtekær Linnet <tlin...@nmr-relax.com
> wrote:
> Hi Sam.
>
> I know your problem. :)
> It is the same for me. Getting hang of a system admin for our lab
> computers, and then to convince him/her
> to fix stuff is not easy.
>
> Thats why I test on Google Cloud.
> There I can get access to a multi core computer, and mess with it.
>
> But it only has a set of standard images. And Fedora is not one of them.
>
> But we can try to have a look at your personal shell setup.
> Can you display your login script?:
>
> One of these should be the right one.
> ---
> cat $HOME/.cshrc
> cat $HOME/.login,
> cat $HOME/.tcshrc
> ---
>
> And now try as well:
> ---
> alias get 'set noglob; wget http://svn.gna.org/viewcvs/*
> checkout*/relax/trunk/devel_scripts/openmpi_test_install_tcsh.sh;unset
> noglob'
> get
>
> # Source functions
> source openmpi_test_install_tcsh.sh
> testopenmpi
> -----
>
> 2016-10-03 18:13 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>:
>
>> Hi Troels,
>>
>> It will be a bit difficult for me to attempt to update, remove, or
>> install any packages since I am not root user, which means I'd have to wait
>> for my PI to come and install/remove packages or programs. Anything
>> regarding installing programs on a user basis I can do (such as installing
>> relax), but I can not for example, install mpi4py. I can download it, untar
>> it, even compile it using the mpicc wrapper, but I cannot install it. I
>> know we discussed the potential problem could be because I have 2 version
>> of relax on my system. Could you try to potentially download another
>> version of relax (the other one I have is 2.2.5) and the older version of
>> openmpi, and attempt to run it then? It would be a lot easier for me to
>> directly tell my PI to simply remove a file, or update one, then to attempt
>> to troubleshoot with them.
>>
>> Sincerely,
>> Sam
>>
>> On Mon, Oct 3, 2016 at 8:58 AM, Troels Emtekær Linnet <
>> tlin...@nmr-relax.com> wrote:
>>
>>> Hi Sam.
>>>
>>> I can get relax to run and work on redhat/centos version 6.
>>>
>>> I have updated a deployment script for this:
>>> http://wiki.nmr-relax.com/Run_relax_at_Google_Cloud_Computin
>>> g#Install_packages_at_server
>>>
>>> Please have a look here:
>>> http://svn.gna.org/viewcvs/relax/trunk/devel_scripts/deploy_scripts/
>>>
>>> and specific:
>>> http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_scri
>>> pts/deploy_scripts/deploy_google_computing_redhat_6_86_x64_u
>>> pgrade_python.sh?content-type=text%2Fplain
>>>
>>> This is for centos 6, which should get very close to fedora 20.
>>>
>>> For centos 6, the openmpi is version 1.8. And you have 1.7.3
>>>
>>> So, the only difference I can see is the openmpi version.
>>> Can you upgrade this?
>>>
>>> ------
>>> [tlinnet@instance-1 ~]$ relax_4.0.2 -i
>>>
>>>
>>>
>>> relax 4.0.2
>>>
>>> Molecular dynamics by NMR data analysis
>>>
>>> Copyright (C) 2001-2006 Edward d'Auvergne
>>> Copyright (C) 2006-2016 the relax development
>>> team
>>>
>>> This is free software which you are welcome to modify and redistribute
>>> under the conditions of the
>>> GNU General Public License (GPL). This program, including all modules,
>>> is licensed under the GPL
>>> and comes with absolutely no warranty. For details type 'GPL' within
>>> the relax prompt.
>>>
>>> Assistance in using the relax prompt and scripting interface can be
>>> accessed by typing 'help' within
>>> the prompt.
>>>
>>> Processor fabric: Uni-processor.
>>>
>>>
>>> Hardware information:
>>> Machine: x86_64
>>> Processor: x86_64
>>> Processor name: Intel(R) Xeon(R) CPU @ 2.50GHz
>>> Endianness: little
>>> Total RAM size: 3426 Mb
>>> Total swap size: 0 Mb
>>>
>>> Operating system information:
>>> System: Linux
>>> Release: 2.6.32-642.4.2.el6.x86_64
>>> Version: #1 SMP Tue Aug 23 19:58:13 UTC 2016
>>> GNU/Linux version: CentOS 6.8 Final
>>> Distribution: centos 6.8 Final
>>> Full platform string: Linux-2.6.32-642.4.2.el6.x86_
>>> 64-x86_64-with-centos-6.8-Final
>>>
>>> Python information:
>>> Architecture: 64bit ELF
>>> Python version: 2.7.8
>>> Python branch:
>>> Python build: default, May 15 2016 12:46:09
>>> Python compiler: GCC 4.4.7 20120313 (Red Hat 4.4.7-16)
>>> Libc version: glibc 2.2.5
>>> Python implementation: CPython
>>> Python revision:
>>> Python executable: /opt/rh/python27/root/usr/bin/python
>>> Python flags: sys.flags(debug=0, py3k_warning=0,
>>> division_warning=0, division_new=0, inspect=0, interactive=0, optimize=0,
>>> dont_write_bytecode=0, no_user_site=0, no_site=0, ignore_environment=0,
>>> tabcheck=0, verbose=0, unicode=0, bytes_warning=0, hash_randomization=0)
>>> Python float info: sys.float_info(max=1.7976931348623157e+308,
>>> max_exp=1024, max_10_exp=308, min=2.2250738585072014e-308, min_exp=-1021,
>>> min_10_exp=-307, dig=15, mant_dig=53, epsilon=2.220446049250313e-16,
>>> radix=2, rounds=1)
>>> Python module path: ['/home/tlinnet/relax-4.0.2',
>>> '/usr/lib64/python2.6/site-packages/openmpi',
>>> '/usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode',
>>> '/opt/rh/python27/root/usr/lib64/python27.zip',
>>> '/opt/rh/python27/root/usr/lib64/python2.7',
>>> '/opt/rh/python27/root/usr/lib64/python2.7/plat-linux2',
>>> '/opt/rh/python27/root/usr/lib64/python2.7/lib-tk',
>>> '/opt/rh/python27/root/usr/lib64/python2.7/lib-old',
>>> '/opt/rh/python27/root/usr/lib64/python2.7/lib-dynload',
>>> '/opt/rh/python27/root/usr/lib64/python2.7/site-packages',
>>> '/opt/rh/python27/root/usr/lib/python2.7/site-packages']
>>>
>>> Python packages and modules (most are optional):
>>>
>>> Name Installed Version Path
>>>
>>> minfx True 1.0.12
>>> /home/tlinnet/relax-4.0.2/minfx
>>> bmrblib True 1.0.4
>>> /home/tlinnet/relax-4.0.2/bmrblib
>>> numpy True 1.7.1
>>> /opt/rh/python27/root/usr/lib64/python2.7/site-packages/numpy
>>> scipy True 0.12.1
>>> /opt/rh/python27/root/usr/lib64/python2.7/site-packages/scipy
>>> wxPython True 2.8.12.0 (gtk2-unicode)
>>> /usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode/wx
>>> matplotlib True 1.5.3
>>> /opt/rh/python27/root/usr/lib64/python2.7/site-packages/matplotlib
>>> mpi4py True 2.0.0
>>> /opt/rh/python27/root/usr/lib64/python2.7/site-packages/mpi4py
>>> epydoc True 3.0.1
>>> /opt/rh/python27/root/usr/lib/python2.7/site-packages/epydoc
>>> optparse True 1.5.3
>>> /opt/rh/python27/root/usr/lib64/python2.7/optparse.pyc
>>> readline True
>>> /opt/rh/python27/root/usr/lib64/python2.7/lib-dynload/readline.so
>>> profile True
>>> /opt/rh/python27/root/usr/lib64/python2.7/profile.pyc
>>> bz2 True
>>> /opt/rh/python27/root/usr/lib64/python2.7/lib-dynload/bz2.so
>>> gzip True
>>> /opt/rh/python27/root/usr/lib64/python2.7/gzip.pyc
>>> io True
>>> /opt/rh/python27/root/usr/lib64/python2.7/io.pyc
>>> xml True 0.8.4 (internal)
>>> /opt/rh/python27/root/usr/lib64/python2.7/xml/__init__.pyc
>>> xml.dom.minidom True
>>> /opt/rh/python27/root/usr/lib64/python2.7/xml/dom/minidom.pyc
>>>
>>> relax information:
>>> Version: 4.0.2
>>> Processor fabric: Uni-processor.
>>>
>>> relax C modules:
>>>
>>> Module Compiled File type
>>> Path
>>>
>>> target_functions.relax_fit True ELF 64-bit LSB shared object,
>>> x86-64, version 1 (SYSV), dynamically linked, not stripped
>>> /home/tlinnet/relax-4.0.2/target_functions/relax_fit.so
>>> ---------
>>>
>>> [tlinnet@instance-1 ~]$ source openmpi_test_install_bash.sh
>>> http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_scri
>>> pts/openmpi_test_install_bash.sh
>>> Source the commands with: source openmpi_test_install_bash.sh
>>> Then do: testopenmpi
>>>
>>> [tlinnet@instance-1 ~]$ testopenmpi
>>> This is functions to test openmpi, python and openmpi.
>>>
>>> Shell is: /bin/bash
>>>
>>> > which mpirun
>>> /usr/lib64/openmpi/bin/mpirun
>>>
>>> > module avail
>>>
>>> --------------------------------------------------------------------------------------
>>> /usr/share/Modules/modulefiles ------------------------------
>>> --------------------------------------------------------
>>> dot module-git module-info modules null use.own
>>>
>>> ------------------------------------------------------------
>>> --------------------------------- /etc/modulefiles
>>> ------------------------------------------------------------
>>> ---------------------------------
>>> openmpi-1.8-x86_64 openmpi-x86_64
>>>
>>> > lscpu
>>> Architecture: x86_64
>>> CPU op-mode(s): 32-bit, 64-bit
>>> Byte Order: Little Endian
>>> CPU(s): 4
>>> On-line CPU(s) list: 0-3
>>> Thread(s) per core: 2
>>> Core(s) per socket: 2
>>> Socket(s): 1
>>> NUMA node(s): 1
>>> Vendor ID: GenuineIntel
>>> CPU family: 6
>>> Model: 62
>>> Model name: Intel(R) Xeon(R) CPU @ 2.50GHz
>>> Stepping: 4
>>> CPU MHz: 2500.000
>>> BogoMIPS: 5000.00
>>> Hypervisor vendor: KVM
>>> Virtualization type: full
>>> L1d cache: 32K
>>> L1i cache: 32K
>>> L2 cache: 256K
>>> L3 cache: 30720K
>>> NUMA node0 CPU(s): 0-3
>>>
>>> > mpirun --version
>>> mpirun (Open MPI) 1.8.1
>>>
>>> Report bugs to http://www.open-mpi.org/community/help/
>>>
>>> > mpirun --report-bindings -np 2 echo "hello world"
>>> hello world
>>> [instance-1:03337] MCW rank 1 bound to socket 0[core 1[hwt 0-1]]: [../BB]
>>> [instance-1:03337] MCW rank 0 bound to socket 0[core 0[hwt 0-1]]: [BB/..]
>>> hello world
>>>
>>> > mpirun --report-bindings -np 2 python -c 'print " Hello " '
>>> [instance-1:03341] MCW rank 1 bound to socket 0[core 1[hwt 0-1]]: [../BB]
>>> [instance-1:03341] MCW rank 0 bound to socket 0[core 0[hwt 0-1]]: [BB/..]
>>> Hello
>>> Hello
>>>
>>> > mpirun --report-bindings -np 2 python --version
>>> [instance-1:03345] MCW rank 1 bound to socket 0[core 1[hwt 0-1]]: [../BB]
>>> [instance-1:03345] MCW rank 0 bound to socket 0[core 0[hwt 0-1]]: [BB/..]
>>> Python 2.7.8
>>> Python 2.7.8
>>>
>>> > mpirun --report-bindings -np 2 /usr/bin/env python --version
>>> [instance-1:03349] MCW rank 1 bound to socket 0[core 1[hwt 0-1]]: [../BB]
>>> [instance-1:03349] MCW rank 0 bound to socket 0[core 0[hwt 0-1]]: [BB/..]
>>> Python 2.7.8
>>> Python 2.7.8
>>>
>>> Testing python, mpi4py and mpirun
>>> Python 2.7.8
>>> Python 2.7.8
>>> 2.0.0
>>> Mpi4py 2.0.0 process 0 of 2 on instance-1.
>>> Mpi4py 2.0.0 process 1 of 2 on instance-1.
>>>
>>> --------
>>>
>>> [tlinnet@instance-1 ~]$ mpirun --np 2 relax_4.0.2 --multi='mpi4py'
>>> --version
>>> relax 4.0.2
>>>
>>>
>>>
>>>
>>>
>>> 2016-10-03 12:39 GMT+02:00 Troels Emtekær Linnet <tlin...@nmr-relax.com>
>>> :
>>>
>>>> Hi Sam.
>>>>
>>>> The commands reflect the BASH shell and not TCSH.
>>>> Thats why there i a little difference.
>>>>
>>>> Can you display your login script?:
>>>>
>>>> One of these should be the right one.
>>>> cat $HOME/.cshrc
>>>> cat $HOME/.login,
>>>> cat $HOME/.tcshrc
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> 2016-10-03 1:50 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>:
>>>>
>>>>> Hi Troels,
>>>>>
>>>>> Here is the output
>>>>> source openmpi_test_install.sh
>>>>> http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_scri
>>>>> pts/openmpi_test_install.sh
>>>>> Source the commands with: source openmpi_test_install.sh
>>>>> Then do: testopenmpi
>>>>>
>>>>> function: Command not found.
>>>>> This is functions to test openmpi, python and openmpi.
>>>>>
>>>>> Shell is: /bin/tcsh
>>>>>
>>>>> > which mpirun
>>>>> mpirun: Command not found.
>>>>>
>>>>> > module avail
>>>>>
>>>>> ------------------------ /usr/share/Modules/modulefiles
>>>>> ------------------------
>>>>> dot module-git module-info modules null use.own
>>>>>
>>>>> ------------------------------- /etc/modulefiles
>>>>> -------------------------------
>>>>> mpi/mpich-x86_64 mpi/openmpi-x86_64 mpich-x86_64
>>>>>
>>>>> > lscpu
>>>>> Architecture: x86_64
>>>>> CPU op-mode(s): 32-bit, 64-bit
>>>>> Byte Order: Little Endian
>>>>> CPU(s): 8
>>>>> On-line CPU(s) list: 0-7
>>>>> Thread(s) per core: 2
>>>>> Core(s) per socket: 4
>>>>> Socket(s): 1
>>>>> NUMA node(s): 1
>>>>> Vendor ID: GenuineIntel
>>>>> CPU family: 6
>>>>> Model: 58
>>>>> Model name: Intel(R) Core(TM) i7-3770S CPU @ 3.10GHz
>>>>> Stepping: 9
>>>>> CPU MHz: 3653.640
>>>>> CPU max MHz: 3900.0000
>>>>> CPU min MHz: 1600.0000
>>>>> BogoMIPS: 6186.25
>>>>> Virtualization: VT-x
>>>>> L1d cache: 32K
>>>>> L1i cache: 32K
>>>>> L2 cache: 256K
>>>>> L3 cache: 8192K
>>>>> NUMA node0 CPU(s): 0-7
>>>>>
>>>>> > mpirun --version
>>>>> mpirun: Command not found.
>>>>>
>>>>> > mpirun --report-bindings -np 2 echo "hello world"
>>>>> mpirun: Command not found.
>>>>>
>>>>> A=": Command not found.
>>>>> A: Undefined variable.
>>>>>
>>>>>
>>>>> The reason the mpi commands didn't work, is becaues openmpi was not
>>>>> loaded. I modified your script (added: module load mpi/openmpi-x86_64)
>>>>> and
>>>>> then got this output
>>>>>
>>>>> source openmpi_test_install.sh
>>>>> http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_scri
>>>>> pts/openmpi_test_install.sh
>>>>> Source the commands with: source openmpi_test_install.sh
>>>>> Then do: testopenmpi
>>>>>
>>>>> function: Command not found.
>>>>> This is functions to test openmpi, python and openmpi.
>>>>>
>>>>> Shell is: /bin/tcsh
>>>>>
>>>>> > which mpirun
>>>>> /usr/lib64/openmpi/bin/mpirun
>>>>>
>>>>> > module avail
>>>>>
>>>>> ------------------------------------ /usr/share/Modules/modulefiles
>>>>> ------------------------------------
>>>>> dot module-git module-info modules null use.own
>>>>>
>>>>> ------------------------------------------- /etc/modulefiles
>>>>> -------------------------------------------
>>>>> mpi/mpich-x86_64 mpi/openmpi-x86_64 mpich-x86_64
>>>>>
>>>>> > lscpu
>>>>> Architecture: x86_64
>>>>> CPU op-mode(s): 32-bit, 64-bit
>>>>> Byte Order: Little Endian
>>>>> CPU(s): 8
>>>>> On-line CPU(s) list: 0-7
>>>>> Thread(s) per core: 2
>>>>> Core(s) per socket: 4
>>>>> Socket(s): 1
>>>>> NUMA node(s): 1
>>>>> Vendor ID: GenuineIntel
>>>>> CPU family: 6
>>>>> Model: 58
>>>>> Model name: Intel(R) Core(TM) i7-3770S CPU @ 3.10GHz
>>>>> Stepping: 9
>>>>> CPU MHz: 3733.320
>>>>> CPU max MHz: 3900.0000
>>>>> CPU min MHz: 1600.0000
>>>>> BogoMIPS: 6186.25
>>>>> Virtualization: VT-x
>>>>> L1d cache: 32K
>>>>> L1i cache: 32K
>>>>> L2 cache: 256K
>>>>> L3 cache: 8192K
>>>>> NUMA node0 CPU(s): 0-7
>>>>>
>>>>> > mpirun --version
>>>>> mpirun (Open MPI) 1.7.3
>>>>>
>>>>> Report bugs to http://www.open-mpi.org/community/help/
>>>>>
>>>>> > mpirun --report-bindings -np 2 echo "hello world"
>>>>> hello world
>>>>> hello world
>>>>>
>>>>> A=": Command not found.
>>>>> A: Undefined variable.
>>>>>
>>>>> As to why the report bindings on python didn't work. I don't know what
>>>>> the A command means, so I don't know what happened there.
>>>>>
>>>>> Sincerely,
>>>>> Sam
>>>>>
>>>>>
>>>>> On Sun, Oct 2, 2016 at 4:16 PM, Troels Emtekær Linnet <
>>>>> tlin...@nmr-relax.com> wrote:
>>>>>
>>>>>> Hi Sam.
>>>>>>
>>>>>> Can you try this in your terminal.
>>>>>> I am trying to write a script, which should check at users setup
>>>>>> mpirun.
>>>>>>
>>>>>> --
>>>>>>
>>>>>> URL=http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_
>>>>>> scripts/openmpi_test_install.sh
>>>>>> wget $URL
>>>>>>
>>>>>> # Source functions
>>>>>> source openmpi_test_install.sh
>>>>>> testopenmpi
>>>>>>
>>>>>> 2016-10-01 0:22 GMT+02:00 Troels Emtekær Linnet <
>>>>>> tlin...@nmr-relax.com>:
>>>>>>
>>>>>>> Hi Sam.
>>>>>>>
>>>>>>> Can you try:
>>>>>>> mpirun --version
>>>>>>>
>>>>>>> Thanks
>>>>>>>
>>>>>>> 2016-10-01 0:00 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>:
>>>>>>>
>>>>>>>> Hi Troels,
>>>>>>>>
>>>>>>>> Here is a list of the packages I got off of the fedora package list
>>>>>>>> Openmpi:
>>>>>>>> openmpi-1.7.3-1.fc.20(64-bit)
>>>>>>>> openmpi-devel-1.7.3-1.fc20(64bit)
>>>>>>>> pypar-openmpi-2.1.5_108_3.fc.20(64bit)
>>>>>>>> python3-mpi4py-1.3.1-1.fc20(64bit)
>>>>>>>>
>>>>>>>> Mpi4py
>>>>>>>> mpi4py-common-1.3.1-1.fc20
>>>>>>>> mpi4py-mpich-1.3.1-1.fc20
>>>>>>>> mpi4py-openmpi-1.3.1-1.fc20
>>>>>>>> python3-mpi4py-mpich-1.3.1-1.fc20
>>>>>>>> python3-mpi4py-openmpi-1.3.1-1.fc20
>>>>>>>>
>>>>>>>> Note: I now know the mpich is extra and pointless. I only use the
>>>>>>>> openmpi when I load my modules. I have not compiled or configured
>>>>>>>> anything
>>>>>>>> with these packages. I just installed them directly from the package
>>>>>>>> list.
>>>>>>>> If you need any more info on what is installed on these computers let
>>>>>>>> me
>>>>>>>> know!
>>>>>>>>
>>>>>>>> Sincerely,
>>>>>>>> Sam
>>>>>>>>
>>>>>>>>
>>>>>>>> On Fri, Sep 30, 2016 at 2:23 PM, Troels Emtekær Linnet <
>>>>>>>> tlin...@nmr-relax.com> wrote:
>>>>>>>>
>>>>>>>>> Hi Sam.
>>>>>>>>>
>>>>>>>>> I am trying to setup myself on Google Cloud Platform.
>>>>>>>>>
>>>>>>>>> Here I setting up for a Redhat 6 distro, in hope it gets close to
>>>>>>>>> Fedora 20.
>>>>>>>>>
>>>>>>>>> I am currently making a deployment script.
>>>>>>>>>
>>>>>>>>> The process is written here:
>>>>>>>>> http://wiki.nmr-relax.com/Run_relax_at_Google_Cloud_Computin
>>>>>>>>> g#Install_packages_at_server
>>>>>>>>>
>>>>>>>>> But that is a little old, since the configurations has changed a
>>>>>>>>> little since 2015.
>>>>>>>>> And the last deployment script is for Ubuntu.
>>>>>>>>>
>>>>>>>>> Getting the packages right is a pain.... ;)
>>>>>>>>>
>>>>>>>>> Let me return when I know some more.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 2016-09-30 23:03 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>:
>>>>>>>>>
>>>>>>>>>> Hi Troels,
>>>>>>>>>>
>>>>>>>>>> I attempted the full path
>>>>>>>>>> mpirun -np 5 ~/relax-4.0.2/relax --multi="mpi4py" -v
>>>>>>>>>> and still got the same result. No output.
>>>>>>>>>>
>>>>>>>>>> Sincerely,
>>>>>>>>>> Sam
>>>>>>>>>>
>>>>>>>>>> On Fri, Sep 30, 2016 at 11:43 AM, Troels Emtekær Linnet <
>>>>>>>>>> tlin...@nmr-relax.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi Sam.
>>>>>>>>>>>
>>>>>>>>>>> Hm. Alright.
>>>>>>>>>>>
>>>>>>>>>>> But to rule it out in my head, can you try this:
>>>>>>>>>>>
>>>>>>>>>>> mpirun -np 5 /home/users/software/relax-4.0.2/relax
>>>>>>>>>>> --multi="mpi4py" -v
>>>>>>>>>>>
>>>>>>>>>>> Or similar destination path.
>>>>>>>>>>> But please try the full path.
>>>>>>>>>>>
>>>>>>>>>>> Best
>>>>>>>>>>> Troels
>>>>>>>>>>>
>>>>>>>>>>> 2016-09-30 19:47 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu
>>>>>>>>>>> >:
>>>>>>>>>>>
>>>>>>>>>>>> I get the same results with the full path mpirun -np 5
>>>>>>>>>>>> ~/relax-4.0.2/relax --multi="mpi4py" -v
>>>>>>>>>>>> Still no output.
>>>>>>>>>>>>
>>>>>>>>>>>> Sincerely,
>>>>>>>>>>>> Sam
>>>>>>>>>>>>
>>>>>>>>>>>> On Fri, Sep 30, 2016 at 10:39 AM, Troels Emtekær Linnet <
>>>>>>>>>>>> tlin...@nmr-relax.com> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Sam.
>>>>>>>>>>>>>
>>>>>>>>>>>>> All points to:
>>>>>>>>>>>>> "./relax" is NOT calling relax in the current folder.
>>>>>>>>>>>>>
>>>>>>>>>>>>> It is because the command "mpirun" is running it.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Please provide the FULL path to relax.
>>>>>>>>>>>>>
>>>>>>>>>>>>> I think I have written this before. ;)
>>>>>>>>>>>>>
>>>>>>>>>>>>> Best
>>>>>>>>>>>>> Troels
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> 2016-09-30 19:24 GMT+02:00 Mahdi, Sam <
>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Sorry, you're right, I re-ran the mpirun -np 5 ./relax
>>>>>>>>>>>>>> --multi="mpi4py" -v
>>>>>>>>>>>>>> and got no output. So I'm just curious for the other
>>>>>>>>>>>>>> computers I download
>>>>>>>>>>>>>> openmpi in, just installing it and compiling it isn't enough?
>>>>>>>>>>>>>> There are
>>>>>>>>>>>>>> some configurations you have to make to have it run on relax?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Sincerely,
>>>>>>>>>>>>>> Sam
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Fri, Sep 30, 2016 at 10:17 AM, Edward d'Auvergne <
>>>>>>>>>>>>>> edw...@nmr-relax.com>
>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> > On 30 September 2016 at 19:12, Mahdi, Sam <
>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>
>>>>>>>>>>>>>> > wrote:
>>>>>>>>>>>>>> > > Hi Edward,
>>>>>>>>>>>>>> > >
>>>>>>>>>>>>>> > > So I ran the the mpirun commands you suggested. The echo
>>>>>>>>>>>>>> world works
>>>>>>>>>>>>>> > fine. I
>>>>>>>>>>>>>> > > get the same results you did. For the relax one, this is
>>>>>>>>>>>>>> the output I
>>>>>>>>>>>>>> > > recieved
>>>>>>>>>>>>>> > > [~/relax-4.0.2]> mpirun -np 5 ./relax --multi="mpi4py"
>>>>>>>>>>>>>> -v relax 4.0.2
>>>>>>>>>>>>>> > > Usage: relax [options] [script_file]
>>>>>>>>>>>>>> > >
>>>>>>>>>>>>>> > > RelaxError: incorrect number of arguments
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> > Have a close look at my original text:
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> > [edward@localhost ~]$ mpirun -np 5
>>>>>>>>>>>>>> /data/relax/tags/4.0.2/relax
>>>>>>>>>>>>>> > --multi="mpi4py" -v
>>>>>>>>>>>>>> > relax 4.0.2
>>>>>>>>>>>>>> > [edward@localhost ~]$
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> > Note how "relax 4.0.2" is on a different line - that is the
>>>>>>>>>>>>>> relax
>>>>>>>>>>>>>> > output, not the command line input. Try again without that
>>>>>>>>>>>>>> text.
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> > > RelaxError: ambiguous option: --v (--verification-tests,
>>>>>>>>>>>>>> --version?)
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> > This is because the double-dash to single-dash conversion
>>>>>>>>>>>>>> is only in
>>>>>>>>>>>>>> > the HTML version of the relax manual, and not emails. Run
>>>>>>>>>>>>>> "relax -h"
>>>>>>>>>>>>>> > to see a description of this option.
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> > > Also, the reason its ./relax is because I have relax
>>>>>>>>>>>>>> 2.2.5 installed,
>>>>>>>>>>>>>> > and I
>>>>>>>>>>>>>> > > have that set up as an Alias, so if I just type relax,
>>>>>>>>>>>>>> it'll open up
>>>>>>>>>>>>>> > relax
>>>>>>>>>>>>>> > > 2.2.5. So I went to the actual relax-4.0.2. directory
>>>>>>>>>>>>>> instead of
>>>>>>>>>>>>>> > indicating
>>>>>>>>>>>>>> > > its path and just typed ./relax. (By I, I mean the
>>>>>>>>>>>>>> administrator of this
>>>>>>>>>>>>>> > > computer, I do not have root access to this computer).
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> > You should set your alias to the relax-4.0.2 version
>>>>>>>>>>>>>> instead. The
>>>>>>>>>>>>>> > 2.2.5 version is very, very old, and many bugs have been
>>>>>>>>>>>>>> fixed since
>>>>>>>>>>>>>> > then.
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> > Regards,
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> > Edward
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> relax (http://www.nmr-relax.com)
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> This is the relax-users mailing list
>>>>>>>>>>>>>> relax-users@gna.org
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> To unsubscribe from this list, get a password
>>>>>>>>>>>>>> reminder, or change your subscription options,
>>>>>>>>>>>>>> visit the list information page at
>>>>>>>>>>>>>> https://mail.gna.org/listinfo/relax-users
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
_______________________________________________
relax (http://www.nmr-relax.com)
This is the relax-users mailing list
relax-users@gna.org
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-users
